Calculation and analysis of the codon pair bias given any set of protein coding genes, calculation of the codon pair score of any gene relative to a codon pair bias, and a versatile gene design algorithm which generates recoded sequences with customized codon pair scores, or random permutations, relative to the codon pair bias of one or two references. The design algorithm also allows for the exclusion of user defined sequence elements during recoding and supports regular expressions. Codon usage and amino acid order are never altered by recoding.
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